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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggacaactgatgttcaagcctcttaacttttgtgaataaagggtttaaagtaaaagtttgctagttaattttcttgtaat...

Basic information

species Oryza sativa
transcript LOC_Os06g07090.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G030144_T01 (Zea mays), 5'ss of exon 6
GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggacaactgatgtt-----caagcctcttaacttttgtgaataaagggtttaaagtaaaagtttgctagttaattttcttgtaat
|||| ||||| |||||| |||| |||||||| ||||||||||||||| ||||||| ||||| |||||| | ||| |||||||||| ||||| ||||| |||||  |      || ||||| |||| ||||| |      ||    | || | | |  || | |||   | |  | | ||| |||  ||  || || | ||     
GTGTGGAGACAATAATGAGCATTGAAGCTACAAGTGGTTTACGTGTGTTGGCAATTAATATTTTGGGTCGGTTTTTGTCCAACCGCGATAACAACATAAGgtagatttgctcttgctcttagacagctgatatggttaacatatttttttaatatattggacaaaaa-tgtggaattaaatttttatatctatttatgttt----

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G017421_T02 (Zea mays), 5'ss of exon 6
GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggacaactgatgttcaagcctcttaacttttgtgaataaagggtttaaagtaaaagtttgctagttaattttcttgtaat--
| || ||||| ||||||||||| |||||||| ||||||||||||||| ||||||| ||||| |||||| | ||| |||||||||||||||| ||||| |||||  |      || ||||| |||| ||||| |      |   |   |||  |  |||| |     || |    || | | |  |  ||||  || |  |  
GCGTGGAGACAATAATGGGCATTGAAGCTACAAGTGGTTTACGTGTGTTGGCAATTAATATTTTGGGTCGTTTTTTGTCCAACCGTGATAACAACATAAGgtagatttgctcttgctcttagacagctgatatggtgatcatattgttttaatatataaggaa--aaaggctggagatagtttttatatttatttattttta

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G23900.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggac---aactgatgttcaagcctcttaacttttgtgaataaagggtttaaagtaaaagtttgctagttaattttcttgtaat
||||||| || || |||| ||| ||||  || | | | || |||||||| || |||||||||||||| |||||  | || ||||| || |||||||||||||  |  || |  | | | |  |    |  ||||  |         | |  | |||   ||| ||   ||   ||   || |  |  ||   | | |  |   
GTGTTGAAACAATCATGGCCATTGAAGACACCAATAGCTTGCGTGTGCTTGCTATCAATATCTTGGGAAGATTCTTATCTAACCGCGACAATAACATCAGgt--tcaaccccctacacctcaattttatttgataatagtatggtattatatatgtttgtaatggaactagcttacttgtatttttcttctgtctatcatct-

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G60070.2 (Arabidopsis thaliana), 5'ss of exon 6
GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggacaactgatgttcaagcctcttaacttttgtgaataaagggtttaa--agtaaaagtttgctagttaattttcttgtaat
| ||| | || |||||| |||||||||  | | ||||  |||| || || |||||||||||||| || | |||  |||||||||| ||||||||||||||||  || |     | |      |     | | ||         |||  | || ||    |   || |   |  | ||  || | | || | |||  | ||| 
GCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAGTCCTTGCAATCAATATCTTAGGAAAATTCTTGTCCAACCGAGATAATAACATCAGgtt-tttatcgagtaccaccatatttgagtttttttttgtaactaatctctgagatcttattattcatctacaataatcttccaaatttagtttgctataa-

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 6
GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcactcttttctcttggacaactgatgttcaagcctctta-acttttgtgaataaagggtttaaagtaa--aagtttgctagttaattttcttgtaat
||||||| ||||| ||| |||| |||| ||||||||| ||||||||||| || |||||||||||||| |||||  |||| || ||||| || || ||||||||| |     || | | ||       ||  |||||| |     |    | | ||    |    |||    | |  |  ||    ||||  | || |  |   
GTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTGTGCTTGCCATCAATATCTTGGGAAGATTCTTGTCAAATCGTGACAACAATATCAGgtaaattttcattattttttat---tttggagttcaacctaggcatgaatatatggtctatttatttttgttgattagattcctaagttgctattatcattgg

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29624901|gb|CB629912.1|CB629912
EST:     GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
EST: gi|58654587|gb|CK043267.1|CK043267
EST:     GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAAT-ACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
EST: gi|29672354|gb|CB668629.1|CB668629
EST:     GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
EST: gi|58673720|gb|CK062406.1|CK062406
EST:     GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
EST: gi|88351874|gb|CI624679.1|CI624679
EST:     GCAATCAATATCTTGGGTAGATCTCTGTACAACCGTGATAATAACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
EST: gi|58655701|gb|CK044381.1|CK044381
EST:     GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAG                         ATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC
genomic: GCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 73 (downstream exon)
Score: 26

GTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTGTGCTGGCAATCAATATCTTGGGTAGATTTCTGTCCAACCGTGATAATAACATCAGgtaattcact ... gtgctttcagATATGTTGCTCTGAACATGCTTATGAAGGCCATGGAGGTAGACACGCAAGCAGTGCAGAGGCATAGAGCAACAATATTAGAGTGTGTCAAG




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